2WSC

Improved Model of Plant Photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.363 
  • R-Value Observed: 0.363 

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This is version 2.0 of the entry. See complete history


Literature

Structure Determination and Improved Model of Plant Photosystem I.

Amunts, A.Toporik, H.Borovikova, A.Nelson, N.

(2010) J Biol Chem 285: 3478

  • DOI: https://doi.org/10.1074/jbc.M109.072645
  • Primary Citation of Related Structures:  
    2WSC, 2WSE, 2WSF, 3LW5

  • PubMed Abstract: 

    Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction. Our current understanding of the sophisticated mechanisms underlying these processes has profited greatly from elucidation of the crystal structures of the Photosystem I complex. In this report, we describe the developments that ultimately led to enhanced structural information of plant Photosystem I. In addition, we report an improved crystallographic model at 3.3-A resolution, which allows analysis of the structure in more detail. An improved electron density map yielded identification and tracing of subunit PsaK. The location of an additional ten beta-carotenes as well as five chlorophylls and several loop regions, which were previously uninterpretable, are now modeled. This represents the most complete plant Photosystem I structure obtained thus far, revealing the locations of and interactions among 17 protein subunits and 193 non-covalently bound photochemical cofactors. Using the new crystal structure, we examine the network of contacts among the protein subunits from the structural perspective, which provide the basis for elucidating the functional organization of the complex.


  • Organizational Affiliation

    Biochemistry Department, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AT3G54890A [auth 1]241Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM IB [auth 2]269Pisum sativumMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA3C [auth 3]276Glycine maxMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTICD [auth 4]251Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1E [auth A]758Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2F [auth B]734Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I IRON-SULFUR CENTERG [auth C]81Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTICH [auth D]212Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTICI [auth E]143Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTICJ [auth F]231Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTICK [auth G]167Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTICL [auth H]144Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT VIIIM [auth I]40Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT IXN [auth J]44Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTICO [auth K]131Hordeum vulgareMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTICP [auth L]216Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I-N SUBUNITQ [auth N]170Phaseolus vulgarisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I-N SUBUNIT53Pisum sativumMutation(s): 0 
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AB [auth 2]
AC [auth 3]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth 2],
AC [auth 3],
AD [auth A],
AE [auth A],
AF [auth A],
AH [auth B],
AJ [auth K],
BB [auth 2],
BC [auth 3],
BD [auth A],
BE [auth A],
BF [auth A],
BH [auth B],
BJ [auth K],
CB [auth 2],
CC [auth 3],
CD [auth A],
CE [auth A],
CF [auth A],
CH [auth B],
CJ [auth K],
DB [auth 2],
DC [auth 3],
DD [auth A],
DE [auth A],
DH [auth B],
DJ [auth L],
EB [auth 2],
ED [auth A],
EE [auth A],
EH [auth B],
EJ [auth L],
FA [auth 1],
FB [auth 2],
FC [auth 4],
FD [auth A],
FE [auth A],
FH [auth B],
FJ [auth L],
GA [auth 1],
GB [auth 2],
GC [auth 4],
GD [auth A],
GE [auth A],
GH [auth B],
GI [auth B],
HA [auth 1],
HB [auth 2],
HC [auth 4],
HD [auth A],
HE [auth A],
HH [auth B],
HI [auth B],
IA [auth 1],
IB [auth 2],
IC [auth 4],
ID [auth A],
IE [auth A],
IG [auth B],
IH [auth B],
II [auth B],
JA [auth 1],
JC [auth 4],
JD [auth A],
JE [auth A],
JG [auth B],
JH [auth B],
JJ [auth L],
KA [auth 1],
KB [auth 2],
KC [auth 4],
KD [auth A],
KE [auth A],
KG [auth B],
KH [auth B],
KJ [auth R],
LA [auth 1],
LB [auth 2],
LC [auth 4],
LD [auth A],
LE [auth A],
LG [auth B],
LH [auth B],
LJ [auth R],
MA [auth 1],
MC [auth 4],
MD [auth A],
ME [auth A],
MG [auth B],
MH [auth B],
MI [auth F],
NA [auth 1],
NC [auth 4],
ND [auth A],
NE [auth A],
NG [auth B],
NH [auth B],
NI [auth F],
OA [auth 1],
OB [auth 3],
OC [auth 4],
OD [auth A],
OG [auth B],
OH [auth B],
OI [auth F],
PA [auth 1],
PB [auth 3],
PC [auth 4],
PD [auth A],
PG [auth B],
PH [auth B],
PI [auth G],
QA [auth 1],
QB [auth 3],
QC [auth 4],
QD [auth A],
QG [auth B],
QH [auth B],
QI [auth H],
RA [auth 1],
RB [auth 3],
RC [auth 4],
RD [auth A],
RG [auth B],
RH [auth B],
RI [auth I],
SA [auth 1],
SB [auth 3],
SC [auth 4],
SD [auth A],
SG [auth B],
SH [auth B],
TA [auth 1],
TB [auth 3],
TD [auth A],
TG [auth B],
TH [auth B],
TI [auth I],
UB [auth 3],
UC [auth 4],
UD [auth A],
UG [auth B],
UI [auth J],
VB [auth 3],
VC [auth 4],
VD [auth A],
VG [auth B],
VI [auth J],
WA [auth 2],
WC [auth 4],
WD [auth A],
WG [auth B],
WI [auth J],
XA [auth 2],
XB [auth 3],
XC [auth A],
XD [auth A],
XE [auth A],
XG [auth B],
XI [auth J],
YA [auth 2],
YB [auth 3],
YC [auth A],
YD [auth A],
YE [auth A],
YG [auth B],
YI [auth K],
ZA [auth 2],
ZB [auth 3],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZG [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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EI [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
BCR
Query on BCR

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AI [auth B]
BI [auth B]
CI [auth B]
GJ [auth L]
HJ [auth L]
AI [auth B],
BI [auth B],
CI [auth B],
GJ [auth L],
HJ [auth L],
PE [auth A],
QE [auth A],
RE [auth A],
SE [auth A],
SI [auth I],
TE [auth A],
UE [auth A],
VH [auth B],
WB [auth 3],
WH [auth B],
XH [auth B],
YH [auth B],
ZH [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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AG [auth A]
BG [auth A]
CG [auth A]
DF [auth A]
DG [auth A]
AG [auth A],
BG [auth A],
CG [auth A],
DF [auth A],
DG [auth A],
DI [auth B],
EC [auth 3],
EF [auth A],
EG [auth A],
FF [auth A],
FG [auth A],
GF [auth A],
GG [auth A],
HF [auth A],
HG [auth A],
IF [auth A],
IJ [auth L],
JB [auth 2],
JF [auth A],
KF [auth A],
LF [auth A],
MB [auth 2],
MF [auth A],
MJ [auth R],
NB [auth 2],
NF [auth A],
NJ [auth R],
OF [auth A],
PF [auth A],
QF [auth A],
RF [auth A],
SF [auth A],
TC [auth 4],
TF [auth A],
UA [auth 1],
UF [auth A],
VA [auth 1],
VE [auth A],
VF [auth A],
WE [auth A],
WF [auth A],
XF [auth A],
YF [auth A],
ZF [auth A],
ZI [auth K]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN

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OE [auth A],
UH [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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FI [auth B],
KI [auth C],
LI [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL
Query on UNL

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JI [auth B]Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.363 
  • R-Value Observed: 0.363 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.655α = 90
b = 189.086β = 91.24
c = 129.388γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MRphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary